HEADER TRANSCRIPTION/INHIBITOR 08-FEB-23 8G4A TITLE HUMAN ARNT PAS-B COMPLEXED WITH KG-548 SMALL MOLECULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ARNT PROTEIN,CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 2, COMPND 5 BHLHE2,DIOXIN RECEPTOR,NUCLEAR TRANSLOCATOR,HYPOXIA-INDUCIBLE FACTOR COMPND 6 1-BETA,HIF-1-BETA,HIF1-BETA; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ARNT, BHLHE2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, TRANSCRIPTION, TRANSCRIPTION-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.XU,E.A.ISIORHO,L.PIMENTEL MARCELINO,K.H.GARDNER REVDAT 1 14-FEB-24 8G4A 0 JRNL AUTH X.XU,K.H.GARDNER JRNL TITL USE OF HIGH PRESSURE NMR SPECTROSCOPY TO RAPIDLY IDENTIFY JRNL TITL 2 PROTEINS WITH INTERNAL LIGAND-BINDING VOIDS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2-3874 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 25028 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.0210 - 1.9700 1.00 1833 148 0.3650 0.3230 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.122 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 61.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.12000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.40000 REMARK 3 B12 (A**2) : -0.06000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 361:465 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.338 -20.952 1.798 REMARK 3 T TENSOR REMARK 3 T11: 0.0657 T22: 0.1531 REMARK 3 T33: 0.0344 T12: -0.0208 REMARK 3 T13: -0.0420 T23: 0.0341 REMARK 3 L TENSOR REMARK 3 L11: 7.5538 L22: 6.7364 REMARK 3 L33: 6.2460 L12: 1.8811 REMARK 3 L13: 0.4882 L23: 0.4778 REMARK 3 S TENSOR REMARK 3 S11: 0.3879 S12: -0.7281 S13: -0.2293 REMARK 3 S21: 0.4571 S22: -0.2342 S23: -0.3638 REMARK 3 S31: 0.1443 S32: -0.1125 S33: -0.1537 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN B AND RESID 360:465 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.434 -12.678 -18.281 REMARK 3 T TENSOR REMARK 3 T11: 0.3590 T22: 0.1621 REMARK 3 T33: 0.0475 T12: -0.0088 REMARK 3 T13: 0.0032 T23: 0.0476 REMARK 3 L TENSOR REMARK 3 L11: 3.5565 L22: 8.4706 REMARK 3 L33: 4.5496 L12: -0.2261 REMARK 3 L13: 0.9897 L23: -1.0778 REMARK 3 S TENSOR REMARK 3 S11: 0.0171 S12: 0.4604 S13: 0.3917 REMARK 3 S21: -1.0189 S22: -0.0355 S23: -0.1055 REMARK 3 S31: -0.1848 S32: 0.3002 S33: 0.0184 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 8G4A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000269265. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27007 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 69.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.8600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 3.82300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: DIAMOND-LIKE APPEARANCE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.5, 1.6 M MAGNESIUM REMARK 280 SULFATE, 2:1 (PROTEIN:CONDITION), VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.57267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.14533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.14533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.57267 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 352 REMARK 465 ALA A 353 REMARK 465 MET A 354 REMARK 465 ASP A 355 REMARK 465 ASN A 356 REMARK 465 VAL A 357 REMARK 465 CYS A 358 REMARK 465 GLN A 359 REMARK 465 PRO A 360 REMARK 465 ASN A 466 REMARK 465 SER A 467 REMARK 465 SER A 468 REMARK 465 GLN A 469 REMARK 465 GLU A 470 REMARK 465 GLY B 352 REMARK 465 ALA B 353 REMARK 465 MET B 354 REMARK 465 ASP B 355 REMARK 465 ASN B 356 REMARK 465 VAL B 357 REMARK 465 CYS B 358 REMARK 465 GLN B 359 REMARK 465 ASN B 466 REMARK 465 SER B 467 REMARK 465 SER B 468 REMARK 465 GLN B 469 REMARK 465 GLU B 470 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 409 0.09 SIDE CHAIN REMARK 500 ARG A 428 0.20 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8G4A A 356 470 UNP P27540 ARNT_HUMAN 356 470 DBREF 8G4A B 356 470 UNP P27540 ARNT_HUMAN 356 470 SEQADV 8G4A GLY A 352 UNP P27540 EXPRESSION TAG SEQADV 8G4A ALA A 353 UNP P27540 EXPRESSION TAG SEQADV 8G4A MET A 354 UNP P27540 EXPRESSION TAG SEQADV 8G4A ASP A 355 UNP P27540 EXPRESSION TAG SEQADV 8G4A GLY B 352 UNP P27540 EXPRESSION TAG SEQADV 8G4A ALA B 353 UNP P27540 EXPRESSION TAG SEQADV 8G4A MET B 354 UNP P27540 EXPRESSION TAG SEQADV 8G4A ASP B 355 UNP P27540 EXPRESSION TAG SEQRES 1 A 119 GLY ALA MET ASP ASN VAL CYS GLN PRO THR GLU PHE ILE SEQRES 2 A 119 SER ARG HIS ASN ILE GLU GLY ILE PHE THR PHE VAL ASP SEQRES 3 A 119 HIS ARG CYS VAL ALA THR VAL GLY TYR GLN PRO GLN GLU SEQRES 4 A 119 LEU LEU GLY LYS ASN ILE VAL GLU PHE CYS HIS PRO GLU SEQRES 5 A 119 ASP GLN GLN LEU LEU ARG ASP SER PHE GLN GLN VAL VAL SEQRES 6 A 119 LYS LEU LYS GLY GLN VAL LEU SER VAL MET PHE ARG PHE SEQRES 7 A 119 ARG SER LYS ASN GLN GLU TRP LEU TRP MET ARG THR SER SEQRES 8 A 119 SER PHE THR PHE GLN ASN PRO TYR SER ASP GLU ILE GLU SEQRES 9 A 119 TYR ILE ILE CYS THR ASN THR ASN VAL LYS ASN SER SER SEQRES 10 A 119 GLN GLU SEQRES 1 B 119 GLY ALA MET ASP ASN VAL CYS GLN PRO THR GLU PHE ILE SEQRES 2 B 119 SER ARG HIS ASN ILE GLU GLY ILE PHE THR PHE VAL ASP SEQRES 3 B 119 HIS ARG CYS VAL ALA THR VAL GLY TYR GLN PRO GLN GLU SEQRES 4 B 119 LEU LEU GLY LYS ASN ILE VAL GLU PHE CYS HIS PRO GLU SEQRES 5 B 119 ASP GLN GLN LEU LEU ARG ASP SER PHE GLN GLN VAL VAL SEQRES 6 B 119 LYS LEU LYS GLY GLN VAL LEU SER VAL MET PHE ARG PHE SEQRES 7 B 119 ARG SER LYS ASN GLN GLU TRP LEU TRP MET ARG THR SER SEQRES 8 B 119 SER PHE THR PHE GLN ASN PRO TYR SER ASP GLU ILE GLU SEQRES 9 B 119 TYR ILE ILE CYS THR ASN THR ASN VAL LYS ASN SER SER SEQRES 10 B 119 GLN GLU HET YL8 A 501 19 HETNAM YL8 5-[3,5-BIS(TRIFLUOROMETHYL)PHENYL]-2H-TETRAZOLE FORMUL 3 YL8 C9 H4 F6 N4 FORMUL 4 HOH *3(H2 O) HELIX 1 AA1 ARG A 379 GLY A 385 1 7 HELIX 2 AA2 GLN A 387 LEU A 391 5 5 HELIX 3 AA3 ASN A 395 CYS A 400 5 6 HELIX 4 AA4 HIS A 401 LEU A 418 1 18 HELIX 5 AA5 ARG B 379 GLY B 385 1 7 HELIX 6 AA6 GLN B 387 LEU B 391 5 5 HELIX 7 AA7 ASN B 395 CYS B 400 5 6 HELIX 8 AA8 HIS B 401 GLU B 403 5 3 HELIX 9 AA9 ASP B 404 LEU B 418 1 15 SHEET 1 AA1 5 PHE A 373 VAL A 376 0 SHEET 2 AA1 5 GLU A 362 HIS A 367 -1 N ARG A 366 O THR A 374 SHEET 3 AA1 5 TYR A 456 ASN A 463 -1 O ILE A 457 N HIS A 367 SHEET 4 AA1 5 TRP A 436 PHE A 446 -1 N ARG A 440 O THR A 462 SHEET 5 AA1 5 LEU A 423 ARG A 430 -1 N PHE A 427 O MET A 439 SHEET 1 AA2 5 PHE B 373 VAL B 376 0 SHEET 2 AA2 5 GLU B 362 HIS B 367 -1 N ARG B 366 O THR B 374 SHEET 3 AA2 5 ILE B 454 ASN B 463 -1 O ASN B 461 N PHE B 363 SHEET 4 AA2 5 TRP B 436 GLN B 447 -1 N ARG B 440 O THR B 462 SHEET 5 AA2 5 LEU B 423 ARG B 430 -1 N PHE B 429 O LEU B 437 CRYST1 80.135 80.135 100.718 90.00 90.00 120.00 P 31 2 1 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012479 0.007205 0.000000 0.00000 SCALE2 0.000000 0.014409 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009929 0.00000